Coding

by davila7

Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

by davila7

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

by davila7

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

by davila7

Comprehensive toolkit for developing with the CocoIndex library. Use when users need to create data transformation pipelines (flows), write custom functions, or operate flows via CLI or API. Covers building ETL workflows for AI data processing, including embedding documents into vector databases, building knowledge graphs, creating search indexes, or processing data streams with incremental updates.

by davila7

Perform code reviews following Sentry engineering practices. Use when reviewing pull requests, examining code changes, or providing feedback on code quality. Covers security, performance, testing, and design review.

by davila7

Comprehensive code review skill for TypeScript, JavaScript, Python, Swift, Kotlin, Go. Includes automated code analysis, best practice checking, security scanning, and review checklist generation. Use when reviewing pull requests, providing code feedback, identifying issues, or ensuring code quality standards.

by davila7

Create commit messages following Sentry conventions. Use when committing code changes, writing commit messages, or formatting git history. Follows conventional commits with Sentry-specific issue references.

by davila7

Anthropic's method for training harmless AI through self-improvement. Two-phase approach - supervised learning with self-critique/revision, then RLAIF (RL from AI Feedback). Use for safety alignment, reducing harmful outputs without human labels. Powers Claude's safety system.

by davila7

Create pull requests following Sentry conventions. Use when opening PRs, writing PR descriptions, or preparing changes for review. Follows Sentry's code review guidelines.

by davila7

Multi-agent orchestration framework for autonomous AI collaboration. Use when building teams of specialized agents working together on complex tasks, when you need role-based agent collaboration with memory, or for production workflows requiring sequential/hierarchical execution. Built without LangChain dependencies for lean, fast execution.

by davila7

Technical leadership guidance for engineering teams, architecture decisions, and technology strategy. Includes tech debt analyzer, team scaling calculator, engineering metrics frameworks, technology evaluation tools, and ADR templates. Use when assessing technical debt, scaling engineering teams, evaluating technologies, making architecture decisions, establishing engineering metrics, or when user mentions CTO, tech debt, technical debt, team scaling, architecture decisions, technology evaluation, engineering metrics, DORA metrics, or technology strategy.

by davila7

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

by davila7

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

by davila7

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.

by davila7

Remove AI-generated code slop from a branch. Use when cleaning up AI-generated code, removing unnecessary comments, defensive checks, or type casts. Checks diff against main and fixes style inconsistencies.

by davila7

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

by davila7

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

by davila7

Build complex AI systems with declarative programming, optimize prompts automatically, create modular RAG systems and agents with DSPy - Stanford NLP's framework for systematic LM programming

by davila7

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

by davila7

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

by davila7

Systematic error diagnosis and resolution using first-principle analysis. Use when encountering any error message, stack trace, or unexpected behavior. Supports replay functionality to record and reuse solutions.

by davila7

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

by davila7

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

by davila7

Evaluates code generation models across HumanEval, MBPP, MultiPL-E, and 15+ benchmarks with pass@k metrics. Use when benchmarking code models, comparing coding abilities, testing multi-language support, or measuring code generation quality. Industry standard from BigCode Project used by HuggingFace leaderboards.

by davila7

Evaluates LLMs across 60+ academic benchmarks (MMLU, HumanEval, GSM8K, TruthfulQA, HellaSwag). Use when benchmarking model quality, comparing models, reporting academic results, or tracking training progress. Industry standard used by EleutherAI, HuggingFace, and major labs. Supports HuggingFace, vLLM, APIs.

by davila7

Facebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.

by davila7

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

by davila7

Fine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.

by davila7

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

by davila7

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

by davila7

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

by davila7

Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that isn't a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.

by davila7

This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.

by davila7

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

by davila7

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

by davila7

Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.

by davila7

Generate descriptive commit messages by analyzing git diffs. Use when the user asks for help writing commit messages or reviewing staged changes.

by davila7

Post-training 4-bit quantization for LLMs with minimal accuracy loss. Use for deploying large models (70B, 405B) on consumer GPUs, when you need 4× memory reduction with <2% perplexity degradation, or for faster inference (3-4× speedup) vs FP16. Integrates with transformers and PEFT for QLoRA fine-tuning.

by davila7

Expert guidance for GRPO/RL fine-tuning with TRL for reasoning and task-specific model training

by davila7

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

by davila7

Control LLM output with regex and grammars, guarantee valid JSON/XML/code generation, enforce structured formats, and build multi-step workflows with Guidance - Microsoft Research's constrained generation framework

by davila7

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

by davila7

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

by davila7

Half-Quadratic Quantization for LLMs without calibration data. Use when quantizing models to 4/3/2-bit precision without needing calibration datasets, for fast quantization workflows, or when deploying with vLLM or HuggingFace Transformers.

by davila7

Simplest distributed training API. 4 lines to add distributed support to any PyTorch script. Unified API for DeepSpeed/FSDP/Megatron/DDP. Automatic device placement, mixed precision (FP16/BF16/FP8). Interactive config, single launch command. HuggingFace ecosystem standard.

by davila7

Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

by davila7

Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.

by davila7

Implements and trains LLMs using Lightning AI's LitGPT with 20+ pretrained architectures (Llama, Gemma, Phi, Qwen, Mistral). Use when need clean model implementations, educational understanding of architectures, or production fine-tuning with LoRA/QLoRA. Single-file implementations, no abstraction layers.

by davila7

Extract structured data from LLM responses with Pydantic validation, retry failed extractions automatically, parse complex JSON with type safety, and stream partial results with Instructor - battle-tested structured output library

by davila7

Iterate on a PR until CI passes. Use when you need to fix CI failures, address review feedback, or continuously push fixes until all checks are green. Automates the feedback-fix-push-wait cycle.

by davila7

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

by davila7

Compress large language models using knowledge distillation from teacher to student models. Use when deploying smaller models with retained performance, transferring GPT-4 capabilities to open-source models, or reducing inference costs. Covers temperature scaling, soft targets, reverse KLD, logit distillation, and MiniLLM training strategies.

by davila7

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

by davila7

Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.

by davila7

Framework for building LLM-powered applications with agents, chains, and RAG. Supports multiple providers (OpenAI, Anthropic, Google), 500+ integrations, ReAct agents, tool calling, memory management, and vector store retrieval. Use for building chatbots, question-answering systems, autonomous agents, or RAG applications. Best for rapid prototyping and production deployments.

by davila7

LLM observability platform for tracing, evaluation, and monitoring. Use when debugging LLM applications, evaluating model outputs against datasets, monitoring production systems, or building systematic testing pipelines for AI applications.

by davila7

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

by davila7

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

by davila7

Runs LLM inference on CPU, Apple Silicon, and consumer GPUs without NVIDIA hardware. Use for edge deployment, M1/M2/M3 Macs, AMD/Intel GPUs, or when CUDA is unavailable. Supports GGUF quantization (1.5-8 bit) for reduced memory and 4-10× speedup vs PyTorch on CPU.

by davila7

Meta's 7-8B specialized moderation model for LLM input/output filtering. 6 safety categories - violence/hate, sexual content, weapons, substances, self-harm, criminal planning. 94-95% accuracy. Deploy with vLLM, HuggingFace, Sagemaker. Integrates with NeMo Guardrails.

by davila7

Data framework for building LLM applications with RAG. Specializes in document ingestion (300+ connectors), indexing, and querying. Features vector indices, query engines, agents, and multi-modal support. Use for document Q&A, chatbots, knowledge retrieval, or building RAG pipelines. Best for data-centric LLM applications.

by davila7

Large Language and Vision Assistant. Enables visual instruction tuning and image-based conversations. Combines CLIP vision encoder with Vicuna/LLaMA language models. Supports multi-turn image chat, visual question answering, and instruction following. Use for vision-language chatbots or image understanding tasks. Best for conversational image analysis.

by davila7

Extend context windows of transformer models using RoPE, YaRN, ALiBi, and position interpolation techniques. Use when processing long documents (32k-128k+ tokens), extending pre-trained models beyond original context limits, or implementing efficient positional encodings. Covers rotary embeddings, attention biases, interpolation methods, and extrapolation strategies for LLMs.

by davila7

State-space model with O(n) complexity vs Transformers' O(n²). 5× faster inference, million-token sequences, no KV cache. Selective SSM with hardware-aware design. Mamba-1 (d_state=16) and Mamba-2 (d_state=128, multi-head). Models 130M-2.8B on HuggingFace.

by davila7

Product marketing, positioning, GTM strategy, and competitive intelligence. Includes ICP definition, April Dunford positioning methodology, launch playbooks, competitive battlecards, and international market entry guides. Use when developing positioning, planning product launches, creating messaging, analyzing competitors, entering new markets, enabling sales, or when user mentions product marketing, positioning, GTM, go-to-market, competitive analysis, market entry, or sales enablement.

by davila7

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

by davila7

Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.

by davila7

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

by davila7

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

by davila7

Track ML experiments, manage model registry with versioning, deploy models to production, and reproduce experiments with MLflow - framework-agnostic ML lifecycle platform

by davila7

Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.

by davila7

Serverless GPU cloud platform for running ML workloads. Use when you need on-demand GPU access without infrastructure management, deploying ML models as APIs, or running batch jobs with automatic scaling.